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GM trannies are more closely matched than another brands, but there is still a difference in performance. If you are worried about performance, you most likely like to shift anyway so the decision is easy.
I have an A4 but would agree that a 6 speed is more fun to drive. I had to consider that my wife might drive the car from time to time so I went with the A4. Also has alot to do with the type of driving you'll be doing, if its alot of stop and go using the clutch can get old quick.
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If I remember right, the factory listed the 0-60 time for the M6 as 4.8 seconds and the auto was around 5.0 seconds. Quarter mile time was 13.2 for the M6 and about 13.4 for the auto.
If two otherwise identical cars, one an M6 and the other an A4 were side by side projects to see who could build the faster car the A4 would win. The M6 could never overcome a "loose" torque converter in the A4 car. The M6 can be more fun to drive on the street in good conditions, however, with stuck in traffic not being one of them.
Depends on the axle ratio. From everything I've seen, and we are talking about stock-for-stock here, an M6 yield a 0-60 advantage of about .3-.4 secs over the A4 with standard 2.73 axle.
An A4 with the 3:15 "performance" axle will close that gap to about .2 secs.
In both cases, the advantage in the 1/4 mi. will be just slightly greater than the above. This assumes perfect M6 launching and shifting by a very competent driver. In many instances, an A4 will outrun an M6 with if there's a novice behind the wheel.
It should also be noted that GM tunes these cars very conservatively. In other words, GM leaves a lot of horsepower on the table with the factory tune. This goes double for the A4 which can be transformed with a good tune.
With a good tune, an A4 with 3:15 axle will run almost neck-and-neck with an M6 making it a driver's race.
Good luck with your decision! Either way, you can't lose.
The A4 in 90% of cases will win races. Hold foot to floor & steer. I say this b/c "most" drivers can't properly shift the M6. I've been in plenty of performace cars in my life & have 1 (count em) ONE friend that can shift his car properly. His drivetrain is "Mike proofed" as well cause he hammers the snot out of each shift. Most guys can't/won't do this cause they are afraid of tearing up parts...me included. With that said, M6 is great fun to drive ! My A4 w/3.90's & converter is also fun too drive.
I can really tell a difference with my A4 after the tune!!!
No torque mgmt and fast shifts that you can really FEEL!!!
Personally, I think the 6 is more fun on an OPEN road, but if you are subject to driving the car in traffic, you may not like it much. Or at least your leg/knee wont !
From my experience for Manual to beat Auto u got to have very good launch and shifting and alot of ppl will screw it up when they are under pressure. For regular driving Auto is also faster than Manual b/c when driving Manual u will try to shift nice and slow and ended up going slower than Auto.